CZI-CABANA Workshop discussion thread

Hi,
It will be highly appreciated if it is possible to share the recording of yesterday’s session before today’s session since I had missed out the metadata segment of the session due to the difference in our time zones.

I am requesting this since I am a beginner in this area and it will be very difficult for me to follow the next segment.

I had tried for registration but seats were unavailable and hence I had opted for the free-viewing option.

2 Likes

This livestream url doesnt exist anymore. Is there any way how we can refer to the videos post live session?

2 Likes

Hi, will the youtube kink for today program be given

1 Like

If you start the livestream and then pause it - it can be paused for any length of time and you can come back and watch it (ie the next day if time zones are an issue). I tested this last night and even with the stream hiccups the ‘unpaused live’ stream was flawless. If you do not start it when the stream begins, I do not think it is possible to go back and access it. Hope this helps

5 Likes

Today’s Live Stream can be found here:

1 Like

Same for me, the YouTube link is showing as restricted today when yesterday I was able to view it just fine.

Maybe you try searching “QIIME 2” on YouTube

1 Like

The video is now working but the audio is shut down, can you guys listen to it?

Thanks for this chance!

yes i can listen to it, very smoothly

1 Like

Hello @chiara ! I am currently listening to the youtube stream and there is audio. I would suggest checking your personal set up. Hope this helps!

1 Like

To add to the discussion about raw sequences and what is inside;

I think you can check the length of the sequences to see if it is longer than the expected size. Let’s say read length is 2x250. Then, if we have sequences longer than 250 bp, doesn’t it mean that there are barcodes or index or something else?

Also, an option out of Q2, FastQC should show if there are Illumina barcodes in fastq files if I’m remembering correctly.

Lastly, yes, there is not a specific way to tell what is inside our files if it is not delivered with right info.

1 Like

Hi @the_dummy,

I agree on fastqc. To answer your question, not necessarily. It may depend on the prep kit and where are sequencing adapters. In my experience, the length of 250 bp includes everything, sequencing adapters (depending on kit ), barcodes as well as PCR primers and low-quality tails. Hence, for me when I saw 250 bp it means these are as raw as possible (for a 2x250 bp MiSeq run at least)

Cheers

2 Likes

5 posts were split to a new topic: Why not use 100% database identity?

A post was split to a new topic: high chimera rate in dada2

Hi @llenzi,

In that case, I’m mistaken to rely only on my experiences.

Thank you very much!

4 posts were split to a new topic: sequence length variation after dada2

A post was split to a new topic: Fragment insertion tree error

A post was split to a new topic: Tools for alignments

A post was split to a new topic: Measuring representation in a fragment insertion tree

A post was split to a new topic: Databases for mouse and intestinal studies